Categorized CHARMM .doc File Index

Note: Some of the features described in the documents below are enabled or disabled via the use of special keywords at compile time. As a consequence, not all compiled versions of CHARMM XXXVERSIONXXX have all of the features, but they can be added by recompiling the source code.

Must Reads

io.doc I/O of data structures and files
miscom.doc Miscellaneous commands
rtop.doc Residue Topology File
select.doc Use of the atom selection facility
struct.doc Structure manipulation (PSF generation
test.doc Commands to test various things
usage.doc CHARMM command usage

Model Building and Manipulation

corman.doc Commands to manipulate coordinates
crystl.doc Crystal facility
hbuild.doc Construction of hydrogen positions
images.doc Use of periodic or crystal environment
intcor.doc Manipulation of internal coordinates
scalar.doc Scalar command for atom properties

Energy and Minimization

cons.doc Harmonic and other constraints or SHAKE
energy.doc Energy evaluation
ewald.doc Ewald summation
minimiz.doc Description of the minimization methods
mmff.doc Merck Molecular Force Field
nbonds.doc Generation of the non-bonded interaction
parmfile.doc CHARMM energy parameters
pbeq.doc Poisson-Boltzmann Equation Solver
qmmm.doc Quantum and Molecular Mechanical FF

Dynamics and Trajectory Analysis

analys.doc Analysis facility
correl.doc Time series and correlation functions
dynamc.doc Dynamics commands
fourd.doc Simulations in 4D (NMR refinement)
monitor.doc Dihedral transition monitor
mts.doc Multiple time step method
nmr.doc NMR analysis facility
nose.doc Nose-Hoover const T dynamics
pressure.doc Pressure calculation and usage
vibran.doc Vibrational analysis facility

Free Energy Methods

block.doc BLOCK free energy simulation
pert.doc PERT free energy perturbation simulations
perturb.doc Thermodynamic Simulation Method
pdetail.doc Details of TSM perturbation

Special Features

hbonds.doc Generation of hydrogen bonds
mmfp.doc Miscelaneous Mean Field Potential
molvib.doc Molecular vibrational analysis facility
replica.doc REPLICA: molecular system replication
rism.doc Reference Interaction Site Model
sbound.doc Stoichastic boundary
travel.doc Reaction coordinate refinement command
umbrel.doc Umbrella Sampling

System Specific

graphx.doc X11 and PostScript graphics, other formats
parallel.doc Requirements for multiprocessor calculations

Compiling, Testing, and Maintaining

install.doc Compiling the distributed source code
testcase.doc Running the CHARMM testcases
charmm_gen.doc Maintaining multiple CHARMM executables

For Developers Only...

developer.doc Guidelines for developers
changelog.doc Description of changes to CHARMM

CHARMM .doc Homepage

Information and HTML pages provided by:

NIH/DCRT Laboratory for Structural Biology
FDA/CBER/OVRR Biophysics Laboratory
Modified, updated and generalized by C.L. Brooks, III
The Scripps Research Institute

Categorized Command Index / rvenable@deimos.cber.nih.gov / brooks@scripps.edu